SMTL ID : 2iuf.1

The structures of Penicillium vitale catalase: resting state, oxidised state (compound I) and complex with aminotriazole

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.71 Å

Oligo State

homo-tetramer

Ligands

2 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.1: 3 residues within 4Å: Chain B: N.409, E.410, T.411 No protein-ligand interaction detected (PLIP) NAG-NAG.34: 3 residues within 4Å: Chain D: N.409, E.410, T.411 No protein-ligand interaction detected (PLIP)

4 x HDD: CIS-HEME D HYDROXYCHLORIN GAMMA-SPIROLACTONE(Non-covalent)

HDD.2: 26 residues within 4Å: Chain A: R.60, V.62, H.63, R.100, G.119, F.120, A.121, V.134, G.135, N.136, F.141, A.146, F.149, V.209, H.210, F.326, L.342, R.346, S.349, Y.350, T.353, Q.354, R.357 Chain B: F.52, D.53 Ligands: O.6 28 PLIP interactions: 26 interactions with chain A, 1 interactions with chain B, 1 Ligand-Ligand interactions Hydrophobic interactions: A:R.60, A:H.63, A:A.121, A:V.134, A:F.141, A:A.146, A:F.149, A:F.149, A:F.149, A:V.209, A:V.209, A:F.326, A:L.342, A:L.342, A:R.346, A:Y.350, A:Y.350, B:F.52 Hydrogen bonds: A:Q.354 Water bridges: A:R.357, A:R.357 Salt bridges: A:R.60, A:R.100, A:R.357 pi-Stacking: A:H.63, A:F.149 Metal complexes: A:Y.350, O.6 HDD.16: 26 residues within 4Å: Chain A: F.52 Chain B: R.60, A.61, V.62, H.63, R.100, G.119, F.120, A.121, V.134, G.135, N.136, F.141, A.146, F.149, V.209, H.210, F.326, L.342, R.346, S.349, Y.350, T.353, Q.354, R.357 Ligands: O.19 29 PLIP interactions: 27 interactions with chain B, 1 interactions with chain A, 1 Ligand-Ligand interactions Hydrophobic interactions: B:R.60, B:H.63, B:A.121, B:V.134, B:F.141, B:A.146, B:F.149, B:F.149, B:F.149, B:F.149, B:V.209, B:V.209, B:F.326, B:L.342, B:L.342, B:R.346, B:Y.350, B:Y.350, A:F.52 Hydrogen bonds: B:Q.354 Water bridges: B:R.357, B:R.357 Salt bridges: B:R.60, B:R.100, B:R.357 pi-Stacking: B:H.63, B:F.149 Metal complexes: B:Y.350, O.19 HDD.35: 26 residues within 4Å: Chain C: R.60, V.62, H.63, R.100, G.119, F.120, A.121, V.134, G.135, N.136, F.141, A.146, F.149, V.209, H.210, F.326, L.342, R.346, S.349, Y.350, T.353, Q.354, R.357 Chain D: F.52, D.53 Ligands: O.39 28 PLIP interactions: 26 interactions with chain C, 1 interactions with chain D, 1 Ligand-Ligand interactions Hydrophobic interactions: C:R.60, C:H.63, C:A.121, C:V.134, C:F.141, C:A.146, C:F.149, C:F.149, C:F.149, C:V.209, C:V.209, C:F.326, C:L.342, C:L.342, C:R.346, C:Y.350, C:Y.350, D:F.52 Hydrogen bonds: C:Q.354 Water bridges: C:R.357, C:R.357 Salt bridges: C:R.60, C:R.100, C:R.357 pi-Stacking: C:H.63, C:F.149 Metal complexes: C:Y.350, O.39 HDD.49: 26 residues within 4Å: Chain C: F.52 Chain D: R.60, A.61, V.62, H.63, R.100, G.119, F.120, A.121, V.134, G.135, N.136, F.141, A.146, F.149, V.209, H.210, F.326, L.342, R.346, S.349, Y.350, T.353, Q.354, R.357 Ligands: O.52 28 PLIP interactions: 27 interactions with chain D, 1 interactions with chain C, Hydrophobic interactions: D:R.60, D:H.63, D:A.121, D:V.134, D:F.141, D:A.146, D:F.149, D:F.149, D:F.149, D:F.149, D:V.209, D:V.209, D:F.326, D:L.342, D:L.342, D:R.346, D:Y.350, D:Y.350, C:F.52 Hydrogen bonds: D:Q.354 Water bridges: D:R.357, D:R.357 Salt bridges: D:R.60, D:R.100, D:R.357 pi-Stacking: D:H.63, D:F.149 Metal complexes: D:Y.350

10 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.3: 3 residues within 4Å: Chain A: N.409, T.411, V.412 6 PLIP interactions: 5 interactions with chain A, 1 interactions with chain D Hydrogen bonds: A:N.409, A:T.411, A:T.411 Water bridges: A:Q.407, A:E.410, D:Q.25 NAG.4: 3 residues within 4Å: Chain A: H.510, D.511, N.512 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:D.511 Hydrogen bonds: A:D.511, A:N.512 Water bridges: A:N.512 NAG.5: 3 residues within 4Å: Chain A: D.78, S.80, N.81 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:D.78 Hydrogen bonds: A:N.81 NAG.17: 2 residues within 4Å: Chain B: H.510, N.512 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:H.510 Hydrogen bonds: B:N.512 NAG.18: 3 residues within 4Å: Chain B: D.78, S.80, N.81 No protein-ligand interaction detected (PLIP) NAG.36: 3 residues within 4Å: Chain C: N.409, T.411, V.412 5 PLIP interactions: 1 interactions with chain B, 4 interactions with chain C Water bridges: B:Q.25, C:Q.407, C:E.410 Hydrogen bonds: C:N.409, C:T.411 NAG.37: 3 residues within 4Å: Chain C: H.510, D.511, N.512 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:D.511 Hydrogen bonds: C:D.511, C:N.512 Water bridges: C:N.512 NAG.38: 3 residues within 4Å: Chain C: D.78, S.80, N.81 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:D.78 Hydrogen bonds: C:N.81 NAG.50: 2 residues within 4Å: Chain D: H.510, N.512 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:H.510 Hydrogen bonds: D:N.512 NAG.51: 3 residues within 4Å: Chain D: D.78, S.80, N.81 No protein-ligand interaction detected (PLIP)

4 x O: OXYGEN ATOM(Non-covalent)

O.6: 5 residues within 4Å: Chain A: V.62, H.63, F.149, Y.350 Ligands: HDD.2 No protein-ligand interaction detected (PLIP) O.19: 5 residues within 4Å: Chain B: V.62, H.63, F.149, Y.350 Ligands: HDD.16 No protein-ligand interaction detected (PLIP) O.39: 5 residues within 4Å: Chain C: V.62, H.63, F.149, Y.350 Ligands: HDD.35 No protein-ligand interaction detected (PLIP) O.52: 5 residues within 4Å: Chain D: V.62, H.63, F.149, Y.350 Ligands: HDD.49 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:Y.350

12 x CA: CALCIUM ION(Non-covalent)(Non-functional Binders)

CA.7: 4 residues within 4Å: Chain A: S.652, E.653, R.654, V.657 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:S.652, A:R.654, A:V.657, H2O.28, H2O.28 CA.8: 1 residues within 4Å: Chain A: T.431 5 PLIP interactions: 5 Ligand-Water interactions Metal complexes: H2O.9, H2O.9, H2O.20, H2O.32, H2O.32 CA.20: 4 residues within 4Å: Chain B: S.652, E.653, R.654, V.657 6 PLIP interactions: 3 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:S.652, B:R.654, B:V.657, H2O.56, H2O.56, H2O.56 CA.21: 1 residues within 4Å: Chain B: T.431 5 PLIP interactions: 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:T.431, H2O.2, H2O.3, H2O.37, H2O.49 CA.31: 2 residues within 4Å: Chain A: Q.244 Chain B: Q.244 No protein-ligand interaction detected (PLIP) CA.32: 1 residues within 4Å: Ligands: CA.65 No protein-ligand interaction detected (PLIP) CA.40: 4 residues within 4Å: Chain C: S.652, E.653, R.654, V.657 5 PLIP interactions: 3 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:S.652, C:R.654, C:V.657, H2O.85, H2O.86 CA.41: 1 residues within 4Å: Chain C: T.431 5 PLIP interactions: 5 Ligand-Water interactions Metal complexes: H2O.66, H2O.66, H2O.77, H2O.89, H2O.89 CA.53: 4 residues within 4Å: Chain D: S.652, E.653, R.654, V.657 6 PLIP interactions: 3 interactions with chain D, 3 Ligand-Water interactions Metal complexes: D:S.652, D:R.654, D:V.657, H2O.113, H2O.113, H2O.114 CA.54: 1 residues within 4Å: Chain D: T.431 5 PLIP interactions: 1 interactions with chain D, 4 Ligand-Water interactions Metal complexes: D:T.431, H2O.60, H2O.60, H2O.95, H2O.106 CA.64: 2 residues within 4Å: Chain C: Q.244 Chain D: Q.244 No protein-ligand interaction detected (PLIP) CA.65: 1 residues within 4Å: Ligands: CA.32 No protein-ligand interaction detected (PLIP)

26 x ACT: ACETATE ION(Non-functional Binders)

ACT.9: 8 residues within 4Å: Chain A: V.104, A.105, D.116, V.117, F.142, I.153, V.156 Ligands: F50.10 Ligand excluded by PLIP ACT.11: 5 residues within 4Å: Chain A: V.238, E.240, E.456, F.457, D.460 Ligand excluded by PLIP ACT.12: 6 residues within 4Å: Chain A: F.131, D.132, F.212, P.328, H.330, I.331 Ligand excluded by PLIP ACT.13: 8 residues within 4Å: Chain A: K.234, A.519, F.520, G.521, E.522, T.677, F.678, K.679 Ligand excluded by PLIP ACT.14: 6 residues within 4Å: Chain A: N.10, D.11, Q.12 Chain D: L.390, D.391, N.401 Ligand excluded by PLIP ACT.22: 8 residues within 4Å: Chain B: V.104, A.105, D.116, V.117, F.142, I.153, V.156 Ligands: F50.23 Ligand excluded by PLIP ACT.24: 4 residues within 4Å: Chain B: V.238, E.240, F.457, D.460 Ligand excluded by PLIP ACT.25: 7 residues within 4Å: Chain B: F.131, D.132, I.133, F.212, P.328, H.330, I.331 Ligand excluded by PLIP ACT.26: 9 residues within 4Å: Chain B: K.234, A.519, F.520, G.521, E.522, L.524, T.677, F.678, K.679 Ligand excluded by PLIP ACT.27: 6 residues within 4Å: Chain B: N.10, D.11, Q.12 Chain C: L.390, D.391, N.401 Ligand excluded by PLIP ACT.29: 5 residues within 4Å: Chain B: R.444, W.447, S.486, D.487, N.488 Ligand excluded by PLIP ACT.30: 4 residues within 4Å: Chain B: Q.1, P.96, R.312, R.372 Ligand excluded by PLIP ACT.33: 1 residues within 4Å: Chain B: S.75 Ligand excluded by PLIP ACT.42: 8 residues within 4Å: Chain C: V.104, A.105, D.116, V.117, F.142, I.153, V.156 Ligands: F50.43 Ligand excluded by PLIP ACT.44: 5 residues within 4Å: Chain C: V.238, E.240, E.456, F.457, D.460 Ligand excluded by PLIP ACT.45: 6 residues within 4Å: Chain C: F.131, D.132, F.212, P.328, H.330, I.331 Ligand excluded by PLIP ACT.46: 8 residues within 4Å: Chain C: K.234, A.519, F.520, G.521, E.522, T.677, F.678, K.679 Ligand excluded by PLIP ACT.47: 6 residues within 4Å: Chain B: L.390, D.391, N.401 Chain C: N.10, D.11, Q.12 Ligand excluded by PLIP ACT.55: 8 residues within 4Å: Chain D: V.104, A.105, D.116, V.117, F.142, I.153, V.156 Ligands: F50.56 Ligand excluded by PLIP ACT.57: 4 residues within 4Å: Chain D: V.238, E.240, F.457, D.460 Ligand excluded by PLIP ACT.58: 7 residues within 4Å: Chain D: F.131, D.132, I.133, F.212, P.328, H.330, I.331 Ligand excluded by PLIP ACT.59: 9 residues within 4Å: Chain D: K.234, A.519, F.520, G.521, E.522, L.524, T.677, F.678, K.679 Ligand excluded by PLIP ACT.60: 6 residues within 4Å: Chain A: L.390, D.391, N.401 Chain D: N.10, D.11, Q.12 Ligand excluded by PLIP ACT.62: 5 residues within 4Å: Chain D: R.444, W.447, S.486, D.487, N.488 Ligand excluded by PLIP ACT.63: 4 residues within 4Å: Chain D: Q.1, P.96, R.312, R.372 Ligand excluded by PLIP ACT.66: 1 residues within 4Å: Chain D: S.75 Ligand excluded by PLIP

6 x F50: ETHANEPEROXOIC ACID(Non-covalent)

F50.10: 10 residues within 4Å: Chain A: R.115, D.116, V.117, F.142, T.169, L.188, A.191, M.192, E.465 Ligands: ACT.9 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:F.142, A:L.188, A:A.191 Hydrogen bonds: A:V.117, A:E.465 F50.23: 10 residues within 4Å: Chain B: R.115, D.116, V.117, F.142, T.169, L.188, A.191, M.192, E.465 Ligands: ACT.22 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:F.142, B:L.188, B:A.191 Hydrogen bonds: B:V.117, B:E.465 Water bridges: B:T.169 F50.28: 3 residues within 4Å: Chain B: I.275, M.276, Q.277 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:I.275 Salt bridges: B:K.222 F50.43: 10 residues within 4Å: Chain C: R.115, D.116, V.117, F.142, T.169, L.188, A.191, M.192, E.465 Ligands: ACT.42 7 PLIP interactions: 7 interactions with chain C Hydrophobic interactions: C:F.142, C:L.188, C:A.191 Hydrogen bonds: C:D.116, C:V.117, C:T.169, C:E.465 F50.56: 10 residues within 4Å: Chain D: R.115, D.116, V.117, F.142, T.169, L.188, A.191, M.192, E.465 Ligands: ACT.55 7 PLIP interactions: 7 interactions with chain D Hydrophobic interactions: D:F.142, D:L.188, D:A.191 Hydrogen bonds: D:D.116, D:V.117, D:E.465 Water bridges: D:T.169 F50.61: 3 residues within 4Å: Chain D: I.275, M.276, Q.277 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:I.275 Salt bridges: D:K.222

2 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.15: 3 residues within 4Å: Chain A: I.275, M.276, Q.277 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:Q.277 Hydrogen bonds: A:I.275 MPD.48: 3 residues within 4Å: Chain C: I.275, M.276, Q.277 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:Q.277 Hydrogen bonds: C:I.275

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Alfonso-Prieto, M. et al., The Structures and Electronic Configuration of Compound I Intermediates of Helicobacter Pylori and Penicillium Vitale Catalases Determined by X-Ray Crystallography and Qm/Mm Density Functional Theory Calculations. J.Am.Chem.Soc. (2007)

Release Date

2006-07-10

Peptides

CATALASE: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
E

C
A

D
E

CATALASE

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